TB-Profiler result

Run: ERR4832046
Summary

Run ID: ERR4832046

Sample name:

Date: 01-04-2023 21:17:35

Number of reads: 449326

Percentage reads mapped: 99.33

Strain: lineage2.2.1

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rpoB 761155 p.Ser450Trp missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289043 p.Ser67Pro missense_variant 1.0 pyrazinamide
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 5956 p.Glu239Asp missense_variant 0.17
gyrB 5961 p.Thr241Ile missense_variant 0.14
gyrB 5966 p.Pro243Ser missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765698 c.2332delT frameshift_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781412 c.-148A>G upstream_gene_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416316 c.1032C>G synonymous_variant 0.17
embR 1416323 p.Asn342Thr missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.31
fabG1 1673349 c.-91G>C upstream_gene_variant 0.31
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.27
fabG1 1673587 p.Gly50Arg missense_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918565 p.Leu209Pro missense_variant 0.75
ndh 2103225 c.-183A>C upstream_gene_variant 0.3
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155103 p.Tyr337Asn missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.57
PPE35 2170053 p.Thr187Ser missense_variant 0.57
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067340 c.606G>A synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568856 c.-177C>A upstream_gene_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3877540 p.Tyr323Cys missense_variant 0.15
clpC1 4038254 c.2451G>T synonymous_variant 0.12
clpC1 4039500 p.Leu402Pro missense_variant 0.15
embC 4240655 p.Ala265Pro missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245348 p.Ala706Thr missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326126 p.Gly450Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0